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Chris Oostenbrink
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Publications
- 2024
- [j50]Matic Broz, Chris Oostenbrink, Urban Bren:
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J. Chem. Inf. Model. 64(6): 2077-2083 (2024) - [j48]Wilfred F. van Gunsteren, Chris Oostenbrink:
Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J. Chem. Inf. Model. 64(16): 6281-6304 (2024) - 2021
- [j44]Jorge Enrique Hernández González, Emir Salas-Sarduy, Lilian Hernández Alvarez, Diego Enry Barreto Gomes, Pedro Geraldo Pascutti, Chris Oostenbrink, Vitor B. P. Leite:
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J. Comput. Aided Mol. Des. 35(10): 1067-1079 (2021) - [j43]Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren:
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. 42(18): 1263-1282 (2021) - 2018
- [j34]Manuela Maurer, Niels Hansen, Chris Oostenbrink:
Comparison of free-energy methods using a tripeptide-water model system. J. Comput. Chem. 39(26): 2226-2242 (2018) - 2016
- [j29]Michael M. H. Graf, Manuela Maurer, Chris Oostenbrink:
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J. Comput. Chem. 37(29): 2597-2605 (2016) - 2015
- [j27]Maria Pechlaner, Chris Oostenbrink:
Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. J. Chem. Inf. Model. 55(12): 2633-2643 (2015) - 2014
- [j20]Ann-Beth Nørholm, Pierre Francotte, Eric Goffin, Iuliana Botez, Laurence Danober, Pierre Lestage, Bernard Pirotte, Jette S. Kastrup, Lars Olsen, Chris Oostenbrink:
Thermodynamic Characterization of New Positive Allosteric Modulators Binding to the Glutamate Receptor A2 Ligand-Binding Domain: Combining Experimental and Computational Methods Unravels Differences in Driving Forces. J. Chem. Inf. Model. 54(12): 3404-3416 (2014) - [j19]Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink:
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. 10(12) (2014) - 2013
- [j18]Michael M. H. Graf, Urban Bren, Dietmar Haltrich, Chris Oostenbrink:
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. J. Comput. Aided Mol. Des. 27(4): 295-304 (2013) - 2012
- [j14]Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren:
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J. Comput. Chem. 33(17): 1467-1477 (2012) - [j13]Urban Bren, Chris Oostenbrink:
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. J. Chem. Inf. Model. 52(6): 1573-1582 (2012) - [j12]Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen:
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. J. Chem. Inf. Model. 52(8): 2139-2148 (2012) - 2011
- [j11]Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren:
Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. 32(9): 1801-1812 (2011) - [j10]Stephanie B. A. De Beer, Alice Glättli, Johannes Hutzler, Nico P. E. Vermeulen, Chris Oostenbrink:
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. J. Comput. Chem. 32(10): 2160-2169 (2011) - 2010
- [j9]Rita Santos, Jozef Hritz, Chris Oostenbrink:
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. J. Chem. Inf. Model. 50(1): 146-154 (2010) - 2009
- [j7]Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink:
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. J. Chem. Inf. Model. 49(1): 43-52 (2009) - 2006
- [j6]Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan:
Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations. J. Comput. Chem. 27(7): 857-867 (2006) - [j5]Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen, Chris Oostenbrink:
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method. J. Chem. Inf. Model. 46(5): 1972-1983 (2006) - 2005
- [j4]Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren:
An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. 26(7): 725-737 (2005) - [j3]Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren:
The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26(16): 1719-1751 (2005) - 2004
- [j2]Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren:
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25(13): 1656-1676 (2004) - 2003
- [j1]Chris Oostenbrink, Wilfred F. van Gunsteren:
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. 24(14): 1730-1739 (2003)
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